The best way to include the notches in the corners of you board is to make them part of your board outline. If they are part of your outline they are not counted as cutouts unless they require routing with a < .062" router. If you have a large hole (< .25") you can include the appropriately sized hole as part of your drill file. If you can't include the information on your drill file you can add it to the board outline layer or on a separate fabrication layer.